plot_comparisons

Plot Conditional or Marginal Comparisons

Description

Plot comparisons on the y-axis against values of one or more predictors (x-axis, colors/shapes, and facets).

The by argument is used to plot marginal comparisons, that is, comparisons made on the original data, but averaged by subgroups. This is analogous to using the by argument in the comparisons() function.

The condition argument is used to plot conditional comparisons, that is, comparisons made on a user-specified grid. This is analogous to using the newdata argument and datagrid() function in a comparisons() call.

All unspecified variables are held at their mean or mode. This includes grouping variables in mixed-effects models, so analysts who fit such models may want to specify the groups of interest using the variables argument, or supply model-specific arguments to compute population-level estimates. See details below. See the "Plots" vignette and website for tutorials and information on how to customize plots:

  • https://vincentarelbundock.github.io/marginaleffects/articles/plot.html

  • https://vincentarelbundock.github.io/marginaleffects

Usage

plot_comparisons(
  model,
  variables = NULL,
  condition = NULL,
  by = NULL,
  newdata = NULL,
  type = "response",
  vcov = NULL,
  conf_level = 0.95,
  wts = NULL,
  comparison = "difference",
  transform = NULL,
  rug = FALSE,
  gray = FALSE,
  draw = TRUE,
  ...
)

Arguments

model

Model object

variables

Name of the variable whose contrast we want to plot on the y-axis.

condition

Conditional slopes

  • Character vector (max length 3): Names of the predictors to display.

  • Named list (max length 3): List names correspond to predictors. List elements can be:

    • Numeric vector

    • Function which returns a numeric vector or a set of unique categorical values

    • Shortcut strings for common reference values: "minmax", "quartile", "threenum"

  • 1: x-axis. 2: color/shape. 3: facets.

  • Numeric variables in positions 2 and 3 are summarized by Tukey’s five numbers ?stats::fivenum.

by

Aggregate unit-level estimates (aka, marginalize, average over). Valid inputs:

  • FALSE: return the original unit-level estimates.

  • TRUE: aggregate estimates for each term.

  • Character vector of column names in newdata or in the data frame produced by calling the function without the by argument.

  • Data frame with a by column of group labels, and merging columns shared by newdata or the data frame produced by calling the same function without the by argument.

  • See examples below.

newdata

When newdata is NULL, the grid is determined by the condition argument. When newdata is not NULL, the argument behaves in the same way as in the comparisons() function.

type

string indicates the type (scale) of the predictions used to compute contrasts or slopes. This can differ based on the model type, but will typically be a string such as: "response", "link", "probs", or "zero". When an unsupported string is entered, the model-specific list of acceptable values is returned in an error message. When type is NULL, the default value is used. This default is the first model-related row in the marginaleffects:::type_dictionary dataframe.

vcov

Type of uncertainty estimates to report (e.g., for robust standard errors). Acceptable values:

  • FALSE: Do not compute standard errors. This can speed up computation considerably.

  • TRUE: Unit-level standard errors using the default vcov(model) variance-covariance matrix.

  • String which indicates the kind of uncertainty estimates to return.

    • Heteroskedasticity-consistent: “HC”, “HC0”, “HC1”, “HC2”, “HC3”, “HC4”, “HC4m”, “HC5”. See ?sandwich::vcovHC

    • Heteroskedasticity and autocorrelation consistent: “HAC”

    • Mixed-Models degrees of freedom: "satterthwaite", "kenward-roger"

    • Other: “NeweyWest”, “KernHAC”, “OPG”. See the sandwich package documentation.

  • One-sided formula which indicates the name of cluster variables (e.g., ~unit_id). This formula is passed to the cluster argument of the sandwich::vcovCL function.

  • Square covariance matrix

  • Function which returns a covariance matrix (e.g., stats::vcov(model))

conf_level

numeric value between 0 and 1. Confidence level to use to build a confidence interval.

wts

string or numeric: weights to use when computing average contrasts or slopes. These weights only affect the averaging in ⁠avg_*()⁠ or with the by argument, and not the unit-level estimates themselves. Internally, estimates and weights are passed to the weighted.mean() function.

  • string: column name of the weights variable in newdata. When supplying a column name to wts, it is recommended to supply the original data (including the weights variable) explicitly to newdata.

  • numeric: vector of length equal to the number of rows in the original data or in newdata (if supplied).

comparison

How should pairs of predictions be compared? Difference, ratio, odds ratio, or user-defined functions.

  • string: shortcuts to common contrast functions.

    • Supported shortcuts strings: difference, differenceavg, differenceavgwts, dydx, eyex, eydx, dyex, dydxavg, eyexavg, eydxavg, dyexavg, dydxavgwts, eyexavgwts, eydxavgwts, dyexavgwts, ratio, ratioavg, ratioavgwts, lnratio, lnratioavg, lnratioavgwts, lnor, lnoravg, lnoravgwts, expdydx, expdydxavg, expdydxavgwts

    • See the Comparisons section below for definitions of each transformation.

  • function: accept two equal-length numeric vectors of adjusted predictions (hi and lo) and returns a vector of contrasts of the same length, or a unique numeric value.

    • See the Transformations section below for examples of valid functions.

transform

string or function. Transformation applied to unit-level estimates and confidence intervals just before the function returns results. Functions must accept a vector and return a vector of the same length. Support string shortcuts: "exp", "ln"

rug

TRUE displays tick marks on the axes to mark the distribution of raw data.

gray

FALSE grayscale or color plot

draw

TRUE returns a ggplot2 plot. FALSE returns a data.frame of the underlying data.

...

Additional arguments are passed to the predict() method supplied by the modeling package.These arguments are particularly useful for mixed-effects or bayesian models (see the online vignettes on the marginaleffects website). Available arguments can vary from model to model, depending on the range of supported arguments by each modeling package. See the "Model-Specific Arguments" section of the ?marginaleffects documentation for a non-exhaustive list of available arguments.

Value

A ggplot2 object

Model-Specific Arguments

Some model types allow model-specific arguments to modify the nature of marginal effects, predictions, marginal means, and contrasts. Please report other package-specific predict() arguments on Github so we can add them to the table below.

https://github.com/vincentarelbundock/marginaleffects/issues

Package Class Argument Documentation
brms brmsfit ndraws brms::posterior_predict
re_formula brms::posterior_predict
lme4 merMod re.form lme4::predict.merMod
allow.new.levels lme4::predict.merMod
glmmTMB glmmTMB re.form glmmTMB::predict.glmmTMB
allow.new.levels glmmTMB::predict.glmmTMB
zitype glmmTMB::predict.glmmTMB
mgcv bam exclude mgcv::predict.bam
robustlmm rlmerMod re.form robustlmm::predict.rlmerMod
allow.new.levels robustlmm::predict.rlmerMod
MCMCglmm MCMCglmm ndraws

Examples

library(marginaleffects)

mod <- lm(mpg ~ hp * drat * factor(am), data = mtcars)

plot_comparisons(mod, variables = "hp", condition = "drat")

plot_comparisons(mod, variables = "hp", condition = c("drat", "am"))

plot_comparisons(mod, variables = "hp", condition = list("am", "drat" = 3:5))

plot_comparisons(mod, variables = "am", condition = list("hp", "drat" = range))
Warning: The `am` variable is treated as a categorical (factor) variable, but the
  original data is of class numeric. It is safer and faster to convert
  such variables to factor before fitting the model and calling `slopes`
  functions.
  
  This warning appears once per session.

plot_comparisons(mod, variables = "am", condition = list("hp", "drat" = "threenum"))